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Crystal structure of DBJA (Wild Type Type II P21)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3A2M PDB ENTRY 3A2M
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.9 293 PEG 4000, PH 7.9, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K
Crystal Properties Matthews coefficient Solvent content 2.17 43.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 125.534 α = 90 b = 47.766 β = 93.61 c = 99.41 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 210 2006-10-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.000 Photon Factory AR-NW12A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.89 50 99.5 0.063 4.8 94042 14.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.89 1.96 3.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 3A2M 1.89 32.81 89306 4717 99.29 0.19331 0.19151 0.1914 0.22783 0.2267 RANDOM 28.735
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] 0.06 0.12 -0.02 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.653 r_dihedral_angle_4_deg 20.431 r_dihedral_angle_3_deg 14.541 r_dihedral_angle_1_deg 5.395 r_scangle_it 2.897 r_scbond_it 1.845 r_angle_refined_deg 1.333 r_mcangle_it 1.096 r_mcbond_it 0.694 r_nbtor_refined 0.308
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.653 r_dihedral_angle_4_deg 20.431 r_dihedral_angle_3_deg 14.541 r_dihedral_angle_1_deg 5.395 r_scangle_it 2.897 r_scbond_it 1.845 r_angle_refined_deg 1.333 r_mcangle_it 1.096 r_mcbond_it 0.694 r_nbtor_refined 0.308 r_symmetry_vdw_refined 0.239 r_nbd_refined 0.207 r_symmetry_hbond_refined 0.153 r_xyhbond_nbd_refined 0.137 r_chiral_restr 0.09 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9288 Nucleic Acid Atoms Solvent Atoms 489 Heterogen Atoms 3
Software Software Software Name Purpose REFMAC refinement